Not quite. The outer spacer fits over the plain, unsplined portion of the stub axle, whereas the hub can only fit, naturally, on the splined portion.
The outer spacer is essential in clamping together the hub, spacer, outer bearing, inner spacer and inner bearing. You are right, the nut doesn't cover the thread, but there's plenty of engagement.
It's a good job you discovered this, as if you'd driven with it like it is there's a very good chance of losing a wheel. You MUST fit the missing spacer.